Mega2R-TBLSFilter

TBLSFilter

<p>This list contains named values.  The name corresponds to an SQLite database table.
 The value is a character string of column names from the "named" table that should be fetched.  A table
 is in this list, if not all the database table columns are needed.  The columns for each table are separated
 by commas.</p>

datasets

Uses as input genetic data that have been reformatted
and stored in a 'SQLite' database; this database is initially
created by the standalone 'mega2' C++ program (available freely
from <https://watson.hgen.pitt.edu/register/>). Loads and
manipulates data frames containing genotype, phenotype, and family
information from the input 'SQLite' database, and decompresses
needed subsets of the genotype data, on the fly, in a memory
efficient manner.  We have also created several more functions that
illustrate how to use the data frames as well as perform useful
tasks: these permit one to run the 'pedgene' package to carry out
gene-based association tests on family data using selected marker
subsets, to run the 'SKAT' package to carry out gene-based
association tests using selected marker subsets, to output the
'Mega2R' data as a VCF file and related files (for phenotype and
family data), and to convert the data frames into 'GenABEL'
gwaa.data-class objects.

Daniel E Weeks

Mega2R

Accessing and Processing a 'Mega2' Genetic Database

 University of Pittsburgh

Mega2R-TBLSFilter function

<p>An object of class <code>list</code> of length 7.</p>

Mega2R-TBLSFilter: Mega2R SQLite3 table filter

Description

Usage

Arguments

Format